def test_case(subDir):
imgStack = BeadsImage(subDir, pathDir)
allCircles = imgStack.makeHoughCircles()
allNormDev = imgStack.makeAllLinePlots(allCircles, minRad=30)
profile = RadialProfile(pathDir)
fname = os.path.join(pathDir, subDir, 'test')
profile.drawProfile(allNormDev, fname, nbrCircles=len(allCircles[0]))
def test_case(subDir):
imgStack = BeadsImage(subDir,pathDir)
allCircles = imgStack.makeHoughCircles()
allNormDev = imgStack.makeAllLinePlots(allCircles,minRad=30)
profile = RadialProfile(pathDir)
fname = os.path.join(pathDir,subDir,'test')
profile.drawProfile(allNormDev,fname,nbrCircles = len(allCircles[0]))
def combineExptPlots(pathDir,pklDir,radPlotDir):
pep = 'TentagelNH2_JSPR011_2_EDC_'
packedList = (
[(os.path.join(pklDir,pep+'Before_MeOH_50ms.meanLineProfile.dict.pkl'),'-','blue'),
(os.path.join(pklDir,pep+'deFmoc_MeOH_50ms.meanLineProfile.dict.pkl'),'--','red'),
(os.path.join(pklDir,pep+'Mock1_MeOH_50ms.meanLineProfile.dict.pkl'),'-.','orange'),
(os.path.join(pklDir,pep+'Edman1_MeOH_50ms.meanLineProfile.dict.pkl'),':','green'),
(os.path.join(pklDir,pep+'Edman2_MeOH_50ms.meanLineProfile.dict.pkl'),'-','purple')
])
fname = os.path.join(radPlotDir,'All_'+pep+'radialProfile')
pf = RadialProfile(pathDir)
pf.combinePlots(packedList,fname)
def drawRadialProfile(self,pklTag,fnameTag):
pklF = os.path.join(self.pklDir,self.exptType+pklTag)
fname = os.path.join(self.radPlotDir,self.exptType+'.'+fnameTag)
nbrBeads,lineProfile,stdevProfile = pickle.load(open(pklF))
yPlus,yMinus = self.getYStdev(lineProfile,stdevProfile)
rawXList = lineProfile.keys()
xList = [x/self.xBin for x in rawXList]
yList = lineProfile.values()
pf = RadialProfile(self.pathDir)
ymaxLimit = 1.2*np.amax(yPlus)
ymaxredLimit = 30000
if 'reduced' in pklTag: ylim = ( 0,ymaxredLimit)
else: ylim = (0, ymaxLimit)
pf.drawProfileWstdev(xList,yList,yPlus,yMinus,fname,nbrCircles=nbrBeads,ylim=ylim)
return True
def drawRadialProfile(self, pklTag, fnameTag):
pklF = os.path.join(self.pklDir, self.exptType + pklTag)
fname = os.path.join(self.radPlotDir, self.exptType + '.' + fnameTag)
nbrBeads, lineProfile, stdevProfile = pickle.load(open(pklF))
yPlus, yMinus = self.getYStdev(lineProfile, stdevProfile)
rawXList = lineProfile.keys()
xList = [x / self.xBin for x in rawXList]
yList = lineProfile.values()
pf = RadialProfile(self.pathDir)
ymaxLimit = 1.2 * np.amax(yPlus)
ymaxredLimit = 30000
if 'reduced' in pklTag: ylim = (0, ymaxredLimit)
else: ylim = (0, ymaxLimit)
pf.drawProfileWstdev(xList,
yList,
yPlus,
yMinus,
fname,
nbrCircles=nbrBeads,
ylim=ylim)
return True
def combineExptPlots(pathDir, pklDir, radPlotDir):
pep = 'TentagelNH2_JSPR011_2_EDC_'
packedList = ([
(os.path.join(pklDir,
pep + 'Before_MeOH_50ms.meanLineProfile.dict.pkl'), '-',
'blue'),
(os.path.join(pklDir,
pep + 'deFmoc_MeOH_50ms.meanLineProfile.dict.pkl'), '--',
'red'),
(os.path.join(pklDir,
pep + 'Mock1_MeOH_50ms.meanLineProfile.dict.pkl'), '-.',
'orange'),
(os.path.join(pklDir,
pep + 'Edman1_MeOH_50ms.meanLineProfile.dict.pkl'), ':',
'green'),
(os.path.join(pklDir,
pep + 'Edman2_MeOH_50ms.meanLineProfile.dict.pkl'), '-',
'purple')
])
fname = os.path.join(radPlotDir, 'All_' + pep + 'radialProfile')
pf = RadialProfile(pathDir)
pf.combinePlots(packedList, fname)
